Rats are an important experiment model for many human diseases, many of which have a genetic component. As followup of our previous work demonstrating impressive differences in the phenotypic responses of LEW and F344 rats to various proinflammatory and noninflammatory stimuli, we have begun to develop a genetic linkage map for rats, specifically applicable to these rat strains. We have now identified about 190 polymorphisms that differ in these rat strains and have mapped most of these to specific chromosomes or linkage groups. We have observed impressive conservation of synteny between rat, mouse and human chromosomes. In addition to beginning a study of cosegregation of inflammatory arthritis with the various polymorphisms in F2 intercross progeny of LEW and F344 rats, we studied the segregation of the athymic nude trait in F2 intercross progeny of athymic nude LEW x euthymic F344 rats. We mapped the locus that controls the nude phenotype to rat chromosome 19m approximately 4 cM from the myosin heavy chain locus. Moreover, through extensive genotyping of 11 additional rat strains, we demonstrated that the LER rat arose as an outcross between LEW and BUF rats, and not, as originally reported, as a spontaneous mutation in LEW rats.